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The three-year partnership aims to bring attention to the importance of immunisation.
Te Kaika chief executive Albie Laurence said it had proven that thinking outside of the box, such as its mass vaccination drive at Forsyth Barr Stadium last year, could have good results for the community.
Super Rugby had hundreds of thousands of fans, many of whom were from groups that had low immunisation rates, such as Maori, Pasifika and low-income families, he said.
Highlanders team doctor Asheer Singh was also a medical practitioner at Te Kaika.
Being in partnership would open up a lot of interesting opportunities for Te Kaika, such as sharing its message on the road and at events, such as at school visits, he said.
A lot of people knew what Te Kaika was and what it did, but there was a wider audience that the partnership would allow it to reach.
A partnership between a sports team and a health organisation was a national first, he said.
Highlanders chief executive Roger Clark said players had a limited amount of time they could spend with the community and it was great that they could work towards an issue close to their hearts.
The Highlanders was a diverse team with a lot of players from low--income backgrounds, so they appreciated how important the work Te Kaika did was, he said.
Highlanders Captain Aaron Smith said the team felt "blessed" to be able to work with an organisation that did such important work.
"It’s just a real good thing to be a part of."